Retrosynthetic Planning with Dual Value Networks

Guoqing Liu, Di Xue, Shufang Xie, Yingce Xia, Austin Tripp, Krzysztof Maziarz, Marwin Segler, Tao Qin, Zongzhang Zhang, Tie-Yan Liu
Proceedings of the 40th International Conference on Machine Learning, PMLR 202:22266-22276, 2023.

Abstract

Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro$^{\ast}$, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro$^{\ast}$, and from 5.63 to 4.78 for RetroGraph).

Cite this Paper

BibTeX
@InProceedings{pmlr-v202-liu23as, title = {Retrosynthetic Planning with Dual Value Networks}, author = {Liu, Guoqing and Xue, Di and Xie, Shufang and Xia, Yingce and Tripp, Austin and Maziarz, Krzysztof and Segler, Marwin and Qin, Tao and Zhang, Zongzhang and Liu, Tie-Yan}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, pages = {22266--22276}, year = {2023}, editor = {Krause, Andreas and Brunskill, Emma and Cho, Kyunghyun and Engelhardt, Barbara and Sabato, Sivan and Scarlett, Jonathan}, volume = {202}, series = {Proceedings of Machine Learning Research}, month = {23--29 Jul}, publisher = {PMLR}, pdf = {https://proceedings.mlr.press/v202/liu23as/liu23as.pdf}, url = {https://proceedings.mlr.press/v202/liu23as.html}, abstract = {Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro$^{\ast}$, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro$^{\ast}$, and from 5.63 to 4.78 for RetroGraph).} }
Endnote
%0 Conference Paper %T Retrosynthetic Planning with Dual Value Networks %A Guoqing Liu %A Di Xue %A Shufang Xie %A Yingce Xia %A Austin Tripp %A Krzysztof Maziarz %A Marwin Segler %A Tao Qin %A Zongzhang Zhang %A Tie-Yan Liu %B Proceedings of the 40th International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2023 %E Andreas Krause %E Emma Brunskill %E Kyunghyun Cho %E Barbara Engelhardt %E Sivan Sabato %E Jonathan Scarlett %F pmlr-v202-liu23as %I PMLR %P 22266--22276 %U https://proceedings.mlr.press/v202/liu23as.html %V 202 %X Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro$^{\ast}$, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro$^{\ast}$, and from 5.63 to 4.78 for RetroGraph).
APA
Liu, G., Xue, D., Xie, S., Xia, Y., Tripp, A., Maziarz, K., Segler, M., Qin, T., Zhang, Z. & Liu, T.. (2023). Retrosynthetic Planning with Dual Value Networks. Proceedings of the 40th International Conference on Machine Learning, in Proceedings of Machine Learning Research 202:22266-22276 Available from https://proceedings.mlr.press/v202/liu23as.html.

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